Zinc in PDB 8da0: Crystal Structure of Mamba Alpha-Neurotoxin in Complex with Centi- 3FTX-D09 Antibody

The structure of Crystal Structure of Mamba Alpha-Neurotoxin in Complex with Centi- 3FTX-D09 Antibody, PDB code: 8da0 was solved by S.Pletnev, R.Verardi, E.S.Tully, J.Glanville, P.D.Kwong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.78 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	59.703, 145.537, 64.207, 90, 104.9, 90
R / Rfree (%)	19.6 / 24.9

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>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Mamba Alpha-Neurotoxin in Complex with Centi- 3FTX-D09 Antibody (pdb code 8da0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 18 binding sites of Zinc where determined in the Crystal Structure of Mamba Alpha-Neurotoxin in Complex with Centi- 3FTX-D09 Antibody, PDB code: 8da0:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 18 in the Crystal Structure of Mamba Alpha-Neurotoxin in Complex with Centi- 3FTX-D09 Antibody


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Mamba Alpha-Neurotoxin in Complex with Centi- 3FTX-D09 Antibody within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:24.8 occ:1.00 O A:HOH508 2.0 34.0 1.0 O A:CYS214 2.1 26.4 1.0 O A:HOH417 2.1 16.5 1.0 C A:CYS214 2.9 27.8 1.0 O A:HOH491 3.8 38.4 1.0 O A:HOH533 4.3 34.6 1.0 CA A:CYS214 4.4 28.0 1.0 OD2 A:ASP122 4.5 41.0 1.0 OD1 A:ASP122 4.7 43.9 1.0 N A:CYS214 4.8 24.0 1.0

Zinc binding site 2 out of 18 in the Crystal Structure of Mamba Alpha-Neurotoxin in Complex with Centi- 3FTX-D09 Antibody


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Mamba Alpha-Neurotoxin in Complex with Centi- 3FTX-D09 Antibody within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:26.4 occ:1.00 OD1 B:ASP230 2.1 27.0 1.0 OE1 A:GLU213 2.1 22.8 1.0 CD A:GLU213 2.7 24.1 1.0 OE2 A:GLU213 2.8 22.9 1.0 CG B:ASP230 2.9 30.3 1.0 CB B:ASP230 3.2 29.6 1.0 CB B:THR232 3.9 49.7 1.0 N B:THR232 4.0 40.3 1.0 OG1 B:THR232 4.1 48.2 1.0 OD2 B:ASP230 4.1 31.9 1.0 CG A:GLU213 4.2 22.6 1.0 CA B:THR232 4.4 45.1 1.0 CA B:ASP230 4.6 31.6 1.0 CB A:GLU213 4.7 21.7 1.0 C B:ASP230 4.8 33.4 1.0 N B:LYS231 4.8 39.8 1.0 O A:HOH402 4.9 21.8 1.0 CA A:GLU213 4.9 21.4 1.0 C B:THR232 4.9 43.6 1.0

Zinc binding site 3 out of 18 in the Crystal Structure of Mamba Alpha-Neurotoxin in Complex with Centi- 3FTX-D09 Antibody


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Mamba Alpha-Neurotoxin in Complex with Centi- 3FTX-D09 Antibody within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:56.1 occ:1.00 O A:HOH507 2.2 40.8 1.0 OD2 A:ASP28 2.3 37.1 1.0 O A:ACT309 2.4 52.1 1.0 O A:HOH526 2.4 29.4 1.0 OXT A:ACT309 2.6 52.5 1.0 C A:ACT309 2.8 55.0 1.0 CG A:ASP28 3.0 28.0 1.0 OD1 A:ASP28 3.0 27.6 1.0 CH3 A:ACT309 4.3 52.1 1.0 O A:HOH535 4.3 41.2 1.0 CB A:ASP28 4.4 26.2 1.0 CA A:SER30 4.7 18.6 1.0 CE C:LYS145 4.9 49.1 1.0 N A:SER30 4.9 18.0 1.0 CA A:GLY68 4.9 20.4 1.0

Zinc binding site 4 out of 18 in the Crystal Structure of Mamba Alpha-Neurotoxin in Complex with Centi- 3FTX-D09 Antibody


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Mamba Alpha-Neurotoxin in Complex with Centi- 3FTX-D09 Antibody within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn304 b:27.0 occ:1.00 OE1 A:GLU187 2.1 24.8 1.0 NZ A:LYS183 2.1 27.3 1.0 O A:HOH518 2.5 24.9 1.0 CD A:GLU187 2.8 24.6 1.0 OE2 A:GLU187 2.8 27.2 1.0 CE A:LYS183 3.0 28.8 1.0 CD A:LYS183 4.1 27.8 1.0 CG A:GLU187 4.2 23.3 1.0 CB A:GLU187 4.8 22.8 1.0 CG A:LYS183 4.9 26.9 1.0

Zinc binding site 5 out of 18 in the Crystal Structure of Mamba Alpha-Neurotoxin in Complex with Centi- 3FTX-D09 Antibody


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Mamba Alpha-Neurotoxin in Complex with Centi- 3FTX-D09 Antibody within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn305 b:32.3 occ:1.00 NE2 B:HIS177 1.9 21.6 1.0 O B:HOH424 2.2 19.9 1.0 OD1 A:ASN138 2.2 29.5 1.0 OD1 A:ASN137 2.3 23.1 1.0 O A:HOH499 2.6 23.1 1.0 CD2 B:HIS177 2.9 20.4 1.0 CE1 B:HIS177 3.0 20.9 1.0 CG A:ASN138 3.1 26.7 1.0 CG A:ASN137 3.2 21.8 1.0 ND2 A:ASN137 3.5 22.9 1.0 ND2 A:ASN138 3.5 29.6 1.0 OG A:SER174 4.0 13.3 1.0 O A:HOH413 4.0 29.1 1.0 CG B:HIS177 4.0 20.6 1.0 ND1 B:HIS177 4.0 20.6 1.0 CB A:ASN138 4.3 23.1 1.0 O B:GLY175 4.4 21.7 1.0 OG1 B:THR196 4.5 23.3 1.0 CB A:ASN137 4.5 21.6 1.0 N A:ASN138 4.5 19.8 1.0 O A:HOH464 4.7 12.7 1.0 CA A:ASN137 4.9 19.4 1.0 CA A:ASN138 4.9 20.4 1.0 C A:ASN137 5.0 18.9 1.0 C B:GLY175 5.0 21.5 1.0

Zinc binding site 6 out of 18 in the Crystal Structure of Mamba Alpha-Neurotoxin in Complex with Centi- 3FTX-D09 Antibody


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Mamba Alpha-Neurotoxin in Complex with Centi- 3FTX-D09 Antibody within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn306 b:18.0 occ:1.00 OD2 A:ASP151 1.8 17.4 1.0 O A:ACT308 1.9 17.4 1.0 ND1 A:HIS189 2.1 23.1 1.0 C A:ACT308 2.6 17.6 1.0 OXT A:ACT308 2.6 16.4 1.0 CG A:ASP151 2.9 18.0 1.0 CE1 A:HIS189 3.0 23.9 1.0 CG A:HIS189 3.2 22.7 1.0 CB A:ASP151 3.3 16.9 1.0 CB A:HIS189 3.6 23.1 1.0 CA A:HIS189 3.7 23.0 1.0 OD1 A:ASP151 4.0 18.8 1.0 CH3 A:ACT308 4.0 18.5 1.0 O A:HOH435 4.1 13.1 1.0 NE2 A:HIS189 4.2 22.9 1.0 CD2 A:HIS189 4.3 23.3 1.0 O A:HOH422 4.3 29.2 1.0 O A:LYS188 4.4 24.6 1.0 N A:HIS189 4.5 23.3 1.0 C A:LYS188 4.7 25.1 1.0 CA A:ASP151 4.8 17.1 1.0 C A:HIS189 4.9 23.0 1.0 N A:LYS190 4.9 24.1 1.0 CG1 A:VAL150 4.9 16.2 1.0

Zinc binding site 7 out of 18 in the Crystal Structure of Mamba Alpha-Neurotoxin in Complex with Centi- 3FTX-D09 Antibody


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Mamba Alpha-Neurotoxin in Complex with Centi- 3FTX-D09 Antibody within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn307 b:32.4 occ:1.00 O A:HOH485 2.4 1.4 1.0 O A:HOH523 2.4 6.9 1.0 O B:HOH521 2.5 5.2 1.0 O B:HOH403 2.6 16.4 1.0 OD1 A:ASN210 3.6 32.0 1.0 O B:THR234 3.7 52.5 1.0 N A:ASN210 4.0 20.0 1.0 CA B:LYS231 4.0 43.0 1.0 CG B:LYS231 4.1 47.0 1.0 O B:HOH474 4.1 27.2 1.0 CG A:ASN210 4.1 28.3 1.0 CB B:LYS231 4.2 45.3 1.0 CB A:ASN210 4.3 24.6 1.0 CA A:PHE209 4.5 17.0 1.0 C A:PHE209 4.6 17.4 1.0 C B:THR234 4.7 48.5 1.0 CA A:ASN210 4.8 22.2 1.0 N B:LYS231 4.9 39.8 1.0 O A:SER208 4.9 16.7 1.0

Zinc binding site 8 out of 18 in the Crystal Structure of Mamba Alpha-Neurotoxin in Complex with Centi- 3FTX-D09 Antibody


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Mamba Alpha-Neurotoxin in Complex with Centi- 3FTX-D09 Antibody within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:23.8 occ:1.00 OD2 B:ASP52 2.0 26.9 1.0 NE2 B:HIS58 2.0 17.8 1.0 O B:HOH490 2.1 18.3 1.0 O B:HOH506 2.3 18.0 1.0 CG B:ASP52 3.0 30.1 1.0 CD2 B:HIS58 3.0 17.9 1.0 CE1 B:HIS58 3.0 17.7 1.0 OD1 B:ASP52 3.4 39.8 1.0 ND1 B:HIS58 4.1 17.1 1.0 CG B:HIS58 4.1 16.6 1.0 O B:HOH416 4.2 14.9 1.0 O B:GLY56 4.2 17.1 1.0 CB B:ASP52 4.3 26.8 1.0 CE2 A:PHE94 4.3 27.3 1.0 CA B:GLY56 4.4 18.0 1.0 C B:GLY56 4.5 17.4 1.0 O B:HOH505 4.6 39.5 1.0 CZ A:PHE94 4.7 28.7 1.0

Zinc binding site 9 out of 18 in the Crystal Structure of Mamba Alpha-Neurotoxin in Complex with Centi- 3FTX-D09 Antibody


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Mamba Alpha-Neurotoxin in Complex with Centi- 3FTX-D09 Antibody within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:46.6 occ:1.00 OD2 B:ASP79 2.2 32.9 1.0 O B:HOH484 2.3 44.7 1.0 O B:HOH504 2.4 21.6 1.0 OE1 B:GLU72 2.6 43.0 1.0 O B:HOH402 2.6 38.1 1.0 O B:HOH419 2.9 42.6 1.0 CG B:ASP79 3.0 26.0 1.0 OD1 B:ASP79 3.1 27.5 1.0 CD B:GLU72 3.5 42.8 1.0 OE2 B:GLU72 3.8 48.3 1.0 NE B:ARG19 4.1 24.7 1.0 NH1 B:ARG19 4.1 23.0 1.0 CB B:ASP79 4.4 22.5 1.0 OG B:SER21 4.4 30.5 1.0 CZ B:ARG19 4.6 24.3 1.0 OG B:SER77 4.6 29.4 1.0 CG B:GLU72 4.8 36.7 1.0

Zinc binding site 10 out of 18 in the Crystal Structure of Mamba Alpha-Neurotoxin in Complex with Centi- 3FTX-D09 Antibody


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Mamba Alpha-Neurotoxin in Complex with Centi- 3FTX-D09 Antibody within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:24.7 occ:1.00 OD1 C:ASN137 2.0 20.6 1.0 O C:HOH440 2.0 18.6 1.0 NE2 D:HIS177 2.1 18.8 1.0 O C:ACT307 2.3 15.9 1.0 OD1 C:ASN138 2.4 21.3 1.0 OXT C:ACT307 2.6 16.3 1.0 C C:ACT307 2.7 15.8 1.0 CG C:ASN137 2.9 20.0 1.0 CD2 D:HIS177 3.0 17.7 1.0 ND2 C:ASN137 3.1 22.5 1.0 CE1 D:HIS177 3.2 18.2 1.0 CG C:ASN138 3.3 21.9 1.0 ND2 C:ASN138 3.9 23.4 1.0 OG C:SER174 4.1 12.9 1.0 CG D:HIS177 4.1 17.5 1.0 ND1 D:HIS177 4.2 17.9 1.0 CH3 C:ACT307 4.2 16.4 1.0 CB C:ASN137 4.3 18.9 1.0 O D:GLY175 4.3 19.2 1.0 CB C:ASN138 4.4 20.3 1.0 OG1 D:THR196 4.4 21.9 1.0 N C:ASN138 4.5 18.3 1.0 O C:HOH479 4.7 27.3 1.0 CA C:ASN137 4.8 18.3 1.0 CA D:GLY175 4.8 19.3 1.0 C D:GLY175 4.9 18.7 1.0 CG2 D:THR196 4.9 21.6 1.0 C C:ASN137 4.9 17.9 1.0 CA C:ASN138 5.0 19.9 1.0

J.Glanville, J.Andrade, M.Bellin, S.Kim, S.Pletnev, D.Tsao, R.Verardi, R.Bedi, T.Friede, E.Tully, B.Zhang, T.Bylund, T.Liu, P.D.Kwong. Venom Protection By Antibody From A Snakebite Hyperimmune Subject To Be Published.